specify pipeline directory to obtain config file when sync

nf_core/create.py

@@ -57,7 +57,7 @@ def __init__(
         default_branch=None,
     ):
         self.template_params, skip_paths_keys, self.template_yaml = self.create_param_dict(
-            name, description, author, version, template_yaml_path, plain
+            name, description, author, version, template_yaml_path, plain, outdir if outdir else "."
         )
 
         skippable_paths = {
@@ -90,14 +90,20 @@ def __init__(
             outdir = os.path.join(os.getcwd(), self.template_params["name_noslash"])
         self.outdir = Path(outdir)
 
-    def create_param_dict(self, name, description, author, version, template_yaml_path, plain):
+    def create_param_dict(self, name, description, author, version, template_yaml_path, plain, pipeline_dir):
         """Creates a dictionary of parameters for the new pipeline.
 
         Args:
+            name (str): Name for the pipeline.
+            description (str): Description for the pipeline.
+            author (str): Authors name of the pipeline.
+            version (str): Version flag.
             template_yaml_path (str): Path to YAML file containing template parameters.
+            plain (bool): If true the pipeline template will be initialized plain, without customisation.
+            pipeline_dir (str): Path to the pipeline directory.
         """
         # Try reading config file
-        _, config_yml = nf_core.utils.load_tools_config()
+        _, config_yml = nf_core.utils.load_tools_config(pipeline_dir)
 
         # Obtain template customization info from template yaml file or `.nf-core.yml` config file
         try:

nf_core/sync.py

@@ -82,7 +82,7 @@ def __init__(
         self.gh_repo = gh_repo
         self.pr_url = ""
 
-        self.config_yml_path, self.config_yml = nf_core.utils.load_tools_config()
+        self.config_yml_path, self.config_yml = nf_core.utils.load_tools_config(self.pipeline_dir)
 
         # Throw deprecation warning if template_yaml_path is set
         if template_yaml_path is not None: